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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC vs.
Revision 841 by mmeineke, Wed Oct 29 17:55:28 2003 UTC

# Line 1 | Line 1
1   #include <algorithm>
2 < #include <cstdlib>
2 > #include <stdlib.h>
3   #include <iostream>
4 < #include <cmath>
4 > #include <math.h>
5   #include <string>
6   #include <sprng.h>
7 –
7   #include "SimSetup.hpp"
8   #include "ReadWrite.hpp"
9   #include "parse_me.h"
# Line 22 | Line 21
21   #define NVT_ENS        1
22   #define NPTi_ENS       2
23   #define NPTf_ENS       3
24 < #define NPTim_ENS      4
26 < #define NPTfm_ENS      5
24 > #define NPTxyz_ENS     4
25  
26 +
27   #define FF_DUFF 0
28   #define FF_LJ   1
29   #define FF_EAM  2
# Line 32 | Line 31 | SimSetup::SimSetup(){
31   using namespace std;
32  
33   SimSetup::SimSetup(){
34 +  
35 +  initSuspend = false;
36    isInfoArray = 0;
37    nInfo = 1;
38  
# Line 54 | Line 55 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi
55    info = the_info;
56    nInfo = theNinfo;
57    isInfoArray = 1;
58 +  initSuspend = true;
59   }
60  
61  
# Line 92 | Line 94 | void SimSetup::createSim(void){
94   #endif // is_mpi
95  
96   void SimSetup::createSim(void){
95 –  int i, j, k, globalAtomIndex;
97  
98    // gather all of the information from the Bass file
99  
# Line 102 | Line 103 | void SimSetup::createSim(void){
103  
104    sysObjectsCreation();
105  
105 –  // check on the post processing info
106 –
107 –  finalInfoCheck();
108 –
106    // initialize the system coordinates
107  
108 <  if (!isInfoArray){
108 >  if ( !initSuspend ){
109      initSystemCoords();
110 +
111 +    if( !(globals->getUseInitTime()) )
112 +      info[0].currentTime = 0.0;
113    }  
114  
115 +  // check on the post processing info
116 +
117 +  finalInfoCheck();
118 +
119    // make the output filenames
120  
121    makeOutNames();
# Line 131 | Line 135 | void SimSetup::makeMolecules(void){
135  
136  
137   void SimSetup::makeMolecules(void){
138 <  int k, l;
138 >  int k;
139    int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140    molInit molInfo;
141    DirectionalAtom* dAtom;
# Line 553 | Line 557 | void SimSetup::gatherInfo(void){
557  
558  
559   void SimSetup::gatherInfo(void){
560 <  int i, j, k;
560 >  int i;
561  
562    ensembleCase = -1;
563    ffCase = -1;
# Line 604 | Line 608 | void SimSetup::gatherInfo(void){
608    else if (!strcasecmp(ensemble, "NPTf")){
609      ensembleCase = NPTf_ENS;
610    }
611 <  else if (!strcasecmp(ensemble, "NPTim")){
612 <    ensembleCase = NPTim_ENS;
611 >  else if (!strcasecmp(ensemble, "NPTxyz")){
612 >    ensembleCase = NPTxyz_ENS;
613    }
610 –  else if (!strcasecmp(ensemble, "NPTfm")){
611 –    ensembleCase = NPTfm_ENS;
612 –  }
614    else{
615      sprintf(painCave.errMsg,
616              "SimSetup Warning. Unrecognized Ensemble -> %s, "
# Line 688 | Line 689 | void SimSetup::gatherInfo(void){
689        info[i].thermalTime = globals->getThermalTime();
690      }
691  
692 <    // check for the temperature set flag
692 >    info[i].resetIntegrator = 0;
693 >    if( globals->haveResetTime() ){
694 >      info[i].resetTime = globals->getResetTime();
695 >      info[i].resetIntegrator = 1;
696 >    }
697  
698 +    // check for the temperature set flag
699 +    
700      if (globals->haveTempSet())
701        info[i].setTemp = globals->getTempSet();
702 <
696 <    // get some of the tricky things that may still be in the globals
697 <
698 <    double boxVector[3];
699 <    if (globals->haveBox()){
700 <      boxVector[0] = globals->getBox();
701 <      boxVector[1] = globals->getBox();
702 <      boxVector[2] = globals->getBox();
703 <
704 <      info[i].setBox(boxVector);
705 <    }
706 <    else if (globals->haveDensity()){
707 <      double vol;
708 <      vol = (double) tot_nmol / globals->getDensity();
709 <      boxVector[0] = pow(vol, (1.0 / 3.0));
710 <      boxVector[1] = boxVector[0];
711 <      boxVector[2] = boxVector[0];
712 <
713 <      info[i].setBox(boxVector);
714 <    }
715 <    else{
716 <      if (!globals->haveBoxX()){
717 <        sprintf(painCave.errMsg,
718 <                "SimSetup error, no periodic BoxX size given.\n");
719 <        painCave.isFatal = 1;
720 <        simError();
721 <      }
722 <      boxVector[0] = globals->getBoxX();
723 <
724 <      if (!globals->haveBoxY()){
725 <        sprintf(painCave.errMsg,
726 <                "SimSetup error, no periodic BoxY size given.\n");
727 <        painCave.isFatal = 1;
728 <        simError();
729 <      }
730 <      boxVector[1] = globals->getBoxY();
731 <
732 <      if (!globals->haveBoxZ()){
733 <        sprintf(painCave.errMsg,
734 <                "SimSetup error, no periodic BoxZ size given.\n");
735 <        painCave.isFatal = 1;
736 <        simError();
737 <      }
738 <      boxVector[2] = globals->getBoxZ();
739 <
740 <      info[i].setBox(boxVector);
741 <    }
702 >    
703    }
704 <
704 >  
705    //setup seed for random number generator
706    int seedValue;
707  
# Line 844 | Line 805 | void SimSetup::finalInfoCheck(void){
805          theEst = globals->getEST();
806        }
807  
808 <      info[i].setEcr(theEcr, theEst);
808 >      info[i].setDefaultEcr(theEcr, theEst);
809  
810        if (!globals->haveDielectric()){
811          sprintf(painCave.errMsg,
# Line 889 | Line 850 | void SimSetup::finalInfoCheck(void){
850            theEst = globals->getEST();
851          }
852  
853 <        info[i].setEcr(theEcr, theEst);
853 >        info[i].setDefaultEcr(theEcr, theEst);
854        }
855      }
856    }
# Line 916 | Line 877 | void SimSetup::initSystemCoords(void){
877      if (worldRank == 0){
878   #endif //is_mpi
879        inName = globals->getInitialConfig();
919 –      double* tempDouble = new double[1000000];
880        fileInit = new InitializeFromFile(inName);
881   #ifdef IS_MPI
882      }
# Line 934 | Line 894 | void SimSetup::initSystemCoords(void){
894  
895      sprintf(painCave.errMsg,
896              "Cannot intialize a parallel simulation without an initial configuration file.\n");
897 <    painCave.isFatal;
897 >    painCave.isFatal = 1;;
898      simError();
899  
900   #else
# Line 1160 | Line 1120 | void SimSetup::calcSysValues(void){
1120   }
1121  
1122   void SimSetup::calcSysValues(void){
1123 <  int i, j, k;
1123 >  int i;
1124  
1125    int* molMembershipArray;
1126  
# Line 1259 | Line 1219 | void SimSetup::makeSysArrays(void){
1219  
1220  
1221   void SimSetup::makeSysArrays(void){
1222 <  int i, j, k, l;
1222 >
1223 > #ifndef IS_MPI
1224 >  int k, j;
1225 > #endif // is_mpi
1226 >  int i, l;
1227  
1228    Atom** the_atoms;
1229    Molecule* the_molecules;
# Line 1342 | Line 1306 | void SimSetup::makeIntegrator(void){
1306   void SimSetup::makeIntegrator(void){
1307    int k;
1308  
1309 +  NVE<RealIntegrator>* myNVE = NULL;
1310    NVT<RealIntegrator>* myNVT = NULL;
1311 <  NPTi<RealIntegrator>* myNPTi = NULL;
1312 <  NPTf<RealIntegrator>* myNPTf = NULL;
1313 <  NPTim<RealIntegrator>* myNPTim = NULL;
1349 <  NPTfm<RealIntegrator>* myNPTfm = NULL;
1311 >  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1312 >  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1313 >  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1314    
1315    for (k = 0; k < nInfo; k++){
1316      switch (ensembleCase){
1317        case NVE_ENS:
1318          if (globals->haveZconstraints()){
1319            setupZConstraint(info[k]);
1320 <          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1320 >          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1321          }
1322 <        else
1323 <          new NVE<RealIntegrator>(&(info[k]), the_ff);
1322 >        else{
1323 >          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1324 >        }
1325 >        
1326 >        info->the_integrator = myNVE;
1327          break;
1328  
1329        case NVT_ENS:
# Line 1378 | Line 1345 | void SimSetup::makeIntegrator(void){
1345            painCave.isFatal = 1;
1346            simError();
1347          }
1348 +
1349 +        info->the_integrator = myNVT;
1350          break;
1351  
1352        case NPTi_ENS:
1353          if (globals->haveZconstraints()){
1354            setupZConstraint(info[k]);
1355 <          myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1355 >          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1356          }
1357          else
1358 <          myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1358 >          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1359  
1360          myNPTi->setTargetTemp(globals->getTargetTemp());
1361  
# Line 1419 | Line 1388 | void SimSetup::makeIntegrator(void){
1388            painCave.isFatal = 1;
1389            simError();
1390          }
1391 +
1392 +        info->the_integrator = myNPTi;
1393          break;
1394  
1395        case NPTf_ENS:
1396          if (globals->haveZconstraints()){
1397            setupZConstraint(info[k]);
1398 <          myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1398 >          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399          }
1400          else
1401 <          myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1401 >          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1402  
1403          myNPTf->setTargetTemp(globals->getTargetTemp());
1404  
# Line 1460 | Line 1431 | void SimSetup::makeIntegrator(void){
1431            painCave.isFatal = 1;
1432            simError();
1433          }
1434 +
1435 +        info->the_integrator = myNPTf;
1436          break;
1437  
1438 <      case NPTim_ENS:
1438 >      case NPTxyz_ENS:
1439          if (globals->haveZconstraints()){
1440            setupZConstraint(info[k]);
1441 <          myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1441 >          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1442          }
1443          else
1444 <          myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1444 >          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1445  
1446 <        myNPTim->setTargetTemp(globals->getTargetTemp());
1446 >        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1447  
1448          if (globals->haveTargetPressure())
1449 <          myNPTim->setTargetPressure(globals->getTargetPressure());
1449 >          myNPTxyz->setTargetPressure(globals->getTargetPressure());
1450          else{
1451            sprintf(painCave.errMsg,
1452                    "SimSetup error: If you use a constant pressure\n"
1453                    "    ensemble, you must set targetPressure in the BASS file.\n");
1454            painCave.isFatal = 1;
1455            simError();
1456 <        }
1456 >        }    
1457  
1458          if (globals->haveTauThermostat())
1459 <          myNPTim->setTauThermostat(globals->getTauThermostat());
1459 >          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1460          else{
1461            sprintf(painCave.errMsg,
1462                    "SimSetup error: If you use an NPT\n"
# Line 1493 | Line 1466 | void SimSetup::makeIntegrator(void){
1466          }
1467  
1468          if (globals->haveTauBarostat())
1469 <          myNPTim->setTauBarostat(globals->getTauBarostat());
1469 >          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1470          else{
1471            sprintf(painCave.errMsg,
1472                    "SimSetup error: If you use an NPT\n"
1473                    "    ensemble, you must set tauBarostat.\n");
1501 –          painCave.isFatal = 1;
1502 –          simError();
1503 –        }
1504 –        break;
1505 –
1506 –      case NPTfm_ENS:
1507 –        if (globals->haveZconstraints()){
1508 –          setupZConstraint(info[k]);
1509 –          myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1510 –        }
1511 –        else
1512 –          myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1513 –
1514 –        myNPTfm->setTargetTemp(globals->getTargetTemp());
1515 –
1516 –        if (globals->haveTargetPressure())
1517 –          myNPTfm->setTargetPressure(globals->getTargetPressure());
1518 –        else{
1519 –          sprintf(painCave.errMsg,
1520 –                  "SimSetup error: If you use a constant pressure\n"
1521 –                  "    ensemble, you must set targetPressure in the BASS file.\n");
1474            painCave.isFatal = 1;
1475            simError();
1476          }
1477  
1478 <        if (globals->haveTauThermostat())
1527 <          myNPTfm->setTauThermostat(globals->getTauThermostat());
1528 <        else{
1529 <          sprintf(painCave.errMsg,
1530 <                  "SimSetup error: If you use an NPT\n"
1531 <                  "    ensemble, you must set tauThermostat.\n");
1532 <          painCave.isFatal = 1;
1533 <          simError();
1534 <        }
1535 <
1536 <        if (globals->haveTauBarostat())
1537 <          myNPTfm->setTauBarostat(globals->getTauBarostat());
1538 <        else{
1539 <          sprintf(painCave.errMsg,
1540 <                  "SimSetup error: If you use an NPT\n"
1541 <                  "    ensemble, you must set tauBarostat.\n");
1542 <          painCave.isFatal = 1;
1543 <          simError();
1544 <        }
1478 >        info->the_integrator = myNPTxyz;
1479          break;
1480  
1481        default:
# Line 1615 | Line 1549 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1549    }
1550    theInfo.addProperty(zconsTol);
1551  
1552 <  //set Force Substraction Policy
1552 >  //set Force Subtraction Policy
1553    StringData* zconsForcePolicy = new StringData();
1554    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1555  
# Line 1624 | Line 1558 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1558    }
1559    else{
1560      sprintf(painCave.errMsg,
1561 <            "ZConstraint Warning: User does not set force substraction policy, "
1562 <            "average force substraction policy is used\n");
1561 >            "ZConstraint Warning: User does not set force Subtraction policy, "
1562 >            "PolicyByMass is used\n");
1563      painCave.isFatal = 0;
1564      simError();
1565 <    zconsForcePolicy->setData("BYNUMBER");
1565 >    zconsForcePolicy->setData("BYMASS");
1566    }
1567  
1568    theInfo.addProperty(zconsForcePolicy);
# Line 1666 | Line 1600 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1600      zconsParaData->addItem(tempParaItem);
1601    }
1602  
1603 +  //check the uniqueness of index  
1604 +  if(!zconsParaData->isIndexUnique()){
1605 +    sprintf(painCave.errMsg,
1606 +            "ZConstraint Error: molIndex is not unique\n");
1607 +    painCave.isFatal = 1;
1608 +    simError();
1609 +  }
1610 +
1611    //sort the parameters by index of molecules
1612    zconsParaData->sortByIndex();
1613 <
1613 >  
1614    //push data into siminfo, therefore, we can retrieve later
1615    theInfo.addProperty(zconsParaData);
1616   }

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